1
|
Cipakova I, Jurcik M, Selicky T, Lalakova LO, Jakubikova J, Cipak L. Dysfunction of Gpl1-Gih35-Wdr83 Complex in S. pombe Affects the Splicing of DNA Damage Repair Factors Resulting in Increased Sensitivity to DNA Damage. Int J Mol Sci 2024; 25:4192. [PMID: 38673778 PMCID: PMC11049892 DOI: 10.3390/ijms25084192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Pre-mRNA splicing plays a key role in the regulation of gene expression. Recent discoveries suggest that defects in pre-mRNA splicing, resulting from the dysfunction of certain splicing factors, can impact the expression of genes crucial for genome surveillance mechanisms, including those involved in cellular response to DNA damage. In this study, we analyzed how cells with a non-functional spliceosome-associated Gpl1-Gih35-Wdr83 complex respond to DNA damage. Additionally, we investigated the role of this complex in regulating the splicing of factors involved in DNA damage repair. Our findings reveal that the deletion of any component within the Gpl1-Gih35-Wdr83 complex leads to a significant accumulation of unspliced pre-mRNAs of DNA repair factors. Consequently, mutant cells lacking this complex exhibit increased sensitivity to DNA-damaging agents. These results highlight the importance of the Gpl1-Gih35-Wdr83 complex in regulating the expression of DNA repair factors, thereby protecting the stability of the genome following DNA damage.
Collapse
Affiliation(s)
- Ingrid Cipakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia; (M.J.); (T.S.); (L.O.L.)
| | - Matus Jurcik
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia; (M.J.); (T.S.); (L.O.L.)
| | - Tomas Selicky
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia; (M.J.); (T.S.); (L.O.L.)
| | - Laura Olivia Lalakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia; (M.J.); (T.S.); (L.O.L.)
| | - Jana Jakubikova
- Department of Tumor Immunology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia;
| | - Lubos Cipak
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia; (M.J.); (T.S.); (L.O.L.)
| |
Collapse
|
2
|
Stanković D, Tain LS, Uhlirova M. Xrp1 governs the stress response program to spliceosome dysfunction. Nucleic Acids Res 2024; 52:2093-2111. [PMID: 38303573 PMCID: PMC10954486 DOI: 10.1093/nar/gkae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 small nuclear ribonucleoprotein particles (snRNPs) in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP-deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP-deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction and mediator of the stress-induced cellular senescence program.
Collapse
Affiliation(s)
- Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Luke S Tain
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| |
Collapse
|
3
|
Sun K, Han Y, Li J, Yu S, Huang Y, Zhang Y, Reilly J, Tu J, Gao P, Jia D, Chen X, Hu H, Ren M, Li P, Luo J, Ren X, Zhang X, Shu X, Liu F, Liu M, Tang Z. The splicing factor DHX38 enables retinal development through safeguarding genome integrity. iScience 2023; 26:108103. [PMID: 37867960 PMCID: PMC10589891 DOI: 10.1016/j.isci.2023.108103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/03/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, we demonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control.
Collapse
Affiliation(s)
- Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jingzhen Li
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yangjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jamas Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, Scotland G4 0BA, UK
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Mengmeng Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Pei Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xianqin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, Scotland G4 0BA, UK
| | - Fei Liu
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| |
Collapse
|
4
|
Li S, Chen Y, Guo Y, Xu J, Wang X, Ning W, Ma L, Qu Y, Zhang M, Zhang H. Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas. PeerJ 2023; 11:e15810. [PMID: 37547724 PMCID: PMC10404032 DOI: 10.7717/peerj.15810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/07/2023] [Indexed: 08/08/2023] Open
Abstract
Background Gliomas are the most commonly-detected malignant tumors of the brain. They contain abundant long non-coding RNAs (lncRNAs), which are valuable cancer biomarkers. LncRNAs may be involved in genomic instability; however, their specific role and mechanism in gliomas remains unclear. LncRNAs that are related to genomic instability have not been reported in gliomas. Methods The transcriptome data from The Cancer Genome Atlas (TCGA) database were analyzed. The co-expression network of genomic instability-related lncRNAs and mRNA was established, and the model of genomic instability-related lncRNA was identified by univariate Cox regression and LASSO analyses. Based on the median risk score obtained in the training set, we divided the samples into high-risk and low-risk groups and proved the survival prediction ability of genomic instability-related lncRNA signatures. The results were verified in the external data set. Finally, a real-time quantitative polymerase chain reaction assay was performed to validate the signature. Results The signatures of 17 lncRNAs (LINC01579, AL022344.1, AC025171.5, LINC01116, MIR155HG, AC131097.3, LINC00906, CYTOR, AC015540.1, SLC25A21.AS1, H19, AL133415.1, SNHG18, FOXD3.AS1, LINC02593, AL354919.2 and CRNDE) related to genomic instability were identified. In the internal data set and Gene Expression Omnibus (GEO) external data set, the low-risk group showed better survival than the high-risk group (P < 0.001). In addition, this feature was identified as an independent risk factor, showing its independent prognostic value with different clinical stratifications. The majority of patients in the low-risk group had isocitrate dehydrogenase 1 (IDH1) mutations. The expression levels of these lncRNAs were significantly higher in glioblastoma cell lines than in normal cells. Conclusions Our study shows that the signature of 17 lncRNAs related to genomic instability has prognostic value for gliomas and could provide a potential therapeutic method for glioblastoma.
Collapse
|
5
|
Arif W, Mathur B, Saikali MF, Chembazhi UV, Toohill K, Song YJ, Hao Q, Karimi S, Blue SM, Yee BA, Van Nostrand EL, Bangru S, Guzman G, Yeo GW, Prasanth KV, Anakk S, Cummins CL, Kalsotra A. Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nat Commun 2023; 14:551. [PMID: 36759613 PMCID: PMC9911759 DOI: 10.1038/s41467-023-35932-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/09/2023] [Indexed: 02/11/2023] Open
Abstract
Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it is also crucial for maintaining genome stability. We show that acute liver damage in the setting of targeted SRSF1 deletion in mice is associated with the excessive formation of deleterious RNA-DNA hybrids (R-loops), which induce DNA damage. Combining hepatocyte-specific transcriptome, proteome, and RNA binding analyses, we demonstrate that widespread genotoxic stress following SRSF1 depletion results in global inhibition of mRNA transcription and protein synthesis, leading to impaired metabolism and trafficking of lipids. Lipid accumulation in SRSF1-deficient hepatocytes is followed by necroptotic cell death, inflammation, and fibrosis, resulting in NASH-like liver pathology. Importantly, SRSF1-depleted human liver cancer cells recapitulate this pathogenesis, illustrating a conserved and fundamental role for SRSF1 in preserving genome integrity and tissue homeostasis. Thus, our study uncovers how the accumulation of detrimental R-loops impedes hepatocellular gene expression, triggering metabolic derangements and liver damage.
Collapse
Affiliation(s)
- Waqar Arif
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bhoomika Mathur
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael F Saikali
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Ullas V Chembazhi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Katelyn Toohill
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Saman Karimi
- Department of Pathology, College of Medicine, Cancer Center, University of Illinois Hospital and Health Science Chicago, Chicago, IL, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Grace Guzman
- Department of Pathology, College of Medicine, Cancer Center, University of Illinois Hospital and Health Science Chicago, Chicago, IL, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sayeepriyadarshini Anakk
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
6
|
Liu J, Zhang H, Xia P, Zhu Y, Xu K, Liu Z, Yuan Y. Genome stability‑related lncRNA ZFPM2‑AS1 promotes tumor progression via miR‑3065‑5p/XRCC4 in hepatocellular carcinoma. Int J Oncol 2023; 62:19. [PMID: 36524359 PMCID: PMC9812252 DOI: 10.3892/ijo.2022.5467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have a certain link to genomic stability (GS). However, the regulatory relationship of lncRNAs and GS has not been thoroughly investigated in hepatocellular carcinoma (HCC). In the present study, samples were retrieved from The Cancer Genome Atlas with somatic mutations and lncRNA expression data. Cox regression analysis was used to identify independent prognostic factors. The RNA levels were determined by reverse transcription‑quantitative PCR and protein levels were detected by western blot analysis. Cell Counting Kit‑8 and colony‑formation assays were used to assess cell viability. Cell migration was measured by wound‑healing and Transwell assays. Cell apoptosis and cell‑cycle progression were evaluated by flow cytometry. GS was detected by alkaline comet and chromosomal aberration assays. A xenograft model and lung metastasis model were used to assess the role of zinc finger protein, FOG family member 2 antisense 1 (ZFPM2‑AS1) in tumor growth in vivo. The molecular mechanisms underlying the biological functions of ZFPM2‑AS1 were investigated through bioinformatics prediction, RNA pull‑down and luciferase reporter assays. A total of 85 genomic instability‑related lncRNAs were identified and a prognostic model was developed. The prognostic model exhibited good predictive power (area under the receiver operating characteristic curve, 0.786). ZFPM2‑AS1 was significantly upregulated in tumor tissues (P<0.001) and it promoted DNA damage repair (P<0.01) and tumor progression in vitro and in vivo. Luciferase reporter assays demonstrated that miR‑3065‑5p was able to bind directly with ZFPM2‑AS1 and X‑ray repair cross complementing 4 (XRCC4). ZFPM2‑AS1 upregulated XRCC4 expression by acting as a sponge (P<0.001). In the present study, a prognostic model for HCC was developed and validated, and one lncRNA of its components was experimentally investigated. ZFPM2‑AS1 regulates XRCC4 by sponging miR‑3065‑5p to promote GS and HCC progression.
Collapse
Affiliation(s)
- Jie Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Hao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Peng Xia
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Yimin Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Kequan Xu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Zhisu Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| |
Collapse
|
7
|
Jiang Y, Cong X, Jiang S, Dong Y, Zhao L, Zang Y, Tan M, Li J. Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:597-613. [PMID: 33607295 PMCID: PMC9880816 DOI: 10.1016/j.gpb.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/12/2020] [Accepted: 11/11/2020] [Indexed: 01/31/2023]
Abstract
AMP-activated protein kinase (AMPK) is a conserved energy sensor that plays roles in diverse biological processes via phosphorylating various substrates. Emerging studies have demonstrated the regulatory roles of AMPK in DNA repair, but the underlying mechanisms remain to be fully understood. Herein, using mass spectrometry-based proteomic technologies, we systematically investigate the regulatory network of AMPK in DNA damage response (DDR). Our system-wide phosphoproteome study uncovers a variety of newly-identified potential substrates involved in diverse biological processes, whereas our system-wide histone modification analysis reveals a link between AMPK and histone acetylation. Together with these findings, we discover that AMPK promotes apoptosis by phosphorylating apoptosis-stimulating of p53 protein 2 (ASPP2) in an irradiation (IR)-dependent manner and regulates histone acetylation by phosphorylating histone deacetylase 9 (HDAC9) in an IR-independent manner. Besides, we reveal that disrupting the histone acetylation by the bromodomain BRD4 inhibitor JQ-1 enhances the sensitivity of AMPK-deficient cells to IR. Therefore, our study has provided a resource to investigate the interplay between phosphorylation and histone acetylation underlying the regulatory network of AMPK, which could be beneficial to understand the exact role of AMPK in DDR.
Collapse
Affiliation(s)
- Yuejing Jiang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoji Cong
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangwen Jiang
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Dong
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhao
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Zang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,Corresponding authors.
| | - Minjia Tan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,Corresponding authors.
| | - Jia Li
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China,Corresponding authors.
| |
Collapse
|
8
|
Sherill-Rofe D, Raban O, Findlay S, Rahat D, Unterman I, Samiei A, Yasmeen A, Kaiser Z, Kuasne H, Park M, Foulkes WD, Bloch I, Zick A, Gotlieb WH, Tabach Y, Orthwein A. Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair. NAR Cancer 2022; 4:zcac013. [PMID: 35399185 PMCID: PMC8991968 DOI: 10.1093/narcan/zcac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).
Collapse
Affiliation(s)
- Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oded Raban
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Amber Yasmeen
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Zafir Kaiser
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - William D Foulkes
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Ein-Kerem, Jerusalem 91120, Israel
| | - Walter H Gotlieb
- Division of Gynecology Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| |
Collapse
|
9
|
An added layer of repression for human genes. Nature 2022; 604:41-42. [PMID: 35354969 DOI: 10.1038/d41586-022-00519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Xie J, Wen M, Zhang J, Wang Z, Wang M, Qiu Y, Zhao W, Zhu F, Yao M, Rong ZX, Hu W, Pei Q, Sun X, Li J, Mao Z, Sun L, Tan R. The roles of RNA helicases in DNA damage repair and tumorigenesis reveal precision therapeutic strategies. Cancer Res 2022; 82:872-884. [PMID: 34987058 DOI: 10.1158/0008-5472.can-21-2187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/04/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
DEAD-box RNA helicases belong to a large group of RNA processing factors and play vital roles unwinding RNA helices and in ribosomal RNA biogenesis. Emerging evidence indicates that RNA helicases are associated with genome stability, yet the mechanisms behind this association remain poorly understood. In this study, we performed a comprehensive analysis of RNA helicases using multiplatform proteogenomic databases. Over 50% (28/49) of detected RNA helicases were highly expressed in multiple tumor tissues, and more than 60% (17/28) of tumor-associated members were directly involved in DNA damage repair (DDR). Analysis of repair dynamics revealed that these RNA helicases are engaged in an extensively broad range of DDR pathways. Among these factors is DDX21, which was prominently upregulated in colorectal cancer. The high expression of DDX21 gave rise to frequent chromosome exchange and increased genome fragmentation. Mechanistically, aberrantly high expression of DDX21 triggered inappropriate repair processes by delaying homologous recombination repair and increasing replication stress, leading to genome instability and tumorigenesis. Treatment with distinct chemotherapeutic drugs caused higher lethality to cancer cells with genome fragility induced by DDX21, providing a perspective for treatment of tumors with high DDX21 expression. This study revealed the role of RNA helicases in DNA damage and their associations with cancer, which could expand therapeutic strategies and improve precision treatments for cancer patients with high expression of RNA helicases.
Collapse
Affiliation(s)
- Jinru Xie
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Ming Wen
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Jiao Zhang
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Zheng Wang
- Department of Geriatrics, Central South University
| | - Meng Wang
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Yanfang Qiu
- Center for Molecular Medicine, Central South University
| | - Wenchao Zhao
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Fang Zhu
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| | - Mianfeng Yao
- Department of Stomatology, Xiangya Hospital Central South University
| | - Zhuo-Xian Rong
- Center for Molecular Medicine, Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Wenfeng Hu
- Center for Molecular Medicine, Xiangya Hospital Central South University
| | - Qian Pei
- Xiangya Hospital Central South University
| | - Xiaoxiang Sun
- School of Life Sciences and Technology, Tongji University
| | - Jinchen Li
- Department of Geriatrics, Central South University
| | - Zhiyong Mao
- School of Life Sciences and Technology, Tongji University
| | | | - Rong Tan
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Central South University
| |
Collapse
|
11
|
Dudek KD, Osipovich AB, Cartailler JP, Gu G, Magnuson MA. Insm1, Neurod1, and Pax6 promote murine pancreatic endocrine cell development through overlapping yet distinct RNA transcription and splicing programs. G3-GENES GENOMES GENETICS 2021; 11:6358139. [PMID: 34534285 PMCID: PMC8527475 DOI: 10.1093/g3journal/jkab303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
Insm1, Neurod1, and Pax6 are essential for the formation and function of pancreatic endocrine cells. Here, we report comparative immunohistochemical, transcriptomic, functional enrichment, and RNA splicing analyses of these genes using gene knock-out mice. Quantitative immunohistochemical analysis confirmed that elimination of each of these three factors variably impairs the proliferation, survival, and differentiation of endocrine cells. Transcriptomic analysis revealed that each factor contributes uniquely to the transcriptome although their effects were overlapping. Functional enrichment analysis revealed that genes downregulated by the elimination of Insm1, Neurod1, and Pax6 are commonly involved in mRNA metabolism, chromatin organization, secretion, and cell cycle regulation, and upregulated genes are associated with protein degradation, autophagy, and apoptotic process. Elimination of Insm1, Neurod1, and Pax6 impaired expression of many RNA-binding proteins thereby altering RNA splicing events, including for Syt14 and Snap25, two genes required for insulin secretion. All three factors are necessary for normal splicing of Syt14, and both Insm1 and Pax6 are necessary for the processing of Snap25. Collectively, these data provide new insights into how Insm1, Neurod1, and Pax6 contribute to the formation of functional pancreatic endocrine cells.
Collapse
Affiliation(s)
- Karrie D Dudek
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna B Osipovich
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Guoquing Gu
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A Magnuson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| |
Collapse
|
12
|
Yang C, Georgiou M, Atkinson R, Collin J, Al-Aama J, Nagaraja-Grellscheid S, Johnson C, Ali R, Armstrong L, Mozaffari-Jovin S, Lako M. Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond. Front Cell Dev Biol 2021; 9:700276. [PMID: 34395430 PMCID: PMC8355544 DOI: 10.3389/fcell.2021.700276] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.
Collapse
Affiliation(s)
- Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert Atkinson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jumana Al-Aama
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Colin Johnson
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin Ali
- King's College London, London, United Kingdom
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
13
|
Yang C, Zhang Y, Segar N, Huang C, Zeng P, Tan X, Mao L, Chen Z, Haglund F, Larsson O, Chen Z, Lin Y. Nuclear IGF1R interacts with NuMA and regulates 53BP1‑dependent DNA double‑strand break repair in colorectal cancer. Oncol Rep 2021; 46:168. [PMID: 34165167 PMCID: PMC8250583 DOI: 10.3892/or.2021.8119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Nuclear insulin-like growth factor 1 receptor (nIGF1R) has been associated with poor overall survival and chemotherapy resistance in various types of cancer; however, the underlying mechanism remains unclear. In the present study, immunoprecipitation-coupled mass spectrometry was performed in an IGF1R-overexpressing SW480-OE colorectal cancer cell line to identify the nIGF1R interactome. Network analysis revealed 197 proteins of interest which were involved in several biological pathways, including RNA processing, DNA double-strand break (DSB) repair and SUMOylation pathways. Nuclear mitotic apparatus protein (NuMA) was identified as one of nIGF1R's colocalizing partners. Proximity ligation assay (PLA) revealed different levels of p53-binding protein 1 (53BP1)-NuMA colocalization between IGF1R-positive (R+) and IGF1R-negative (R−) mouse embryonic fibroblasts following exposure to ionizing radiation (IR). 53BP1 was retained by NuMA in the R− cells during IR-induced DNA damage. By contrast, the level of NuMA-53BP1 was markedly lower in R+ cells compared with R− cells. The present data suggested a regulatory role of nIGF1R in 53BP1-dependent DSB repair through its interaction with NuMA. Bright-field PLA analysis on a paraffin-embedded tissue microarray from patients with colorectal cancer revealed a significant association between increased nuclear colocalizing signals of NuMA-53BP1 and a shorter overall survival. These results indicate that nIGF1R plays a role in facilitating 53BP1-dependent DDR by regulating the NuMA-53BP1 interaction, which in turn might affect the clinical outcome of patients with colorectal cancer.
Collapse
Affiliation(s)
- Chen Yang
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Yifan Zhang
- Department of Clinical Pathology and Cytology, Karolinska University Hospital Solna, 171 64 Solna, Stockholm, Sweden
| | - Nelly Segar
- Department of Oncology and Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Changhao Huang
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Pengwei Zeng
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Xiangzhou Tan
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Linfeng Mao
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Zhikang Chen
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Felix Haglund
- Department of Oncology and Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology and Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Zihua Chen
- Department of General Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410000, P.R. China
| | - Yingbo Lin
- Department of Oncology and Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| |
Collapse
|
14
|
Transcriptional Stress Induces Chromatin Relocation of the Nucleotide Excision Repair Factor XPG. Int J Mol Sci 2021; 22:ijms22126589. [PMID: 34205418 PMCID: PMC8235791 DOI: 10.3390/ijms22126589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
Endonuclease XPG participates in nucleotide excision repair (NER), in basal transcription, and in the processing of RNA/DNA hybrids (R-loops): the malfunction of these processes may cause genome instability. Here, we investigate the chromatin association of XPG during basal transcription and after transcriptional stress. The inhibition of RNA polymerase II with 5,6-dichloro-l-β-D-ribofuranosyl benzimidazole (DRB), or actinomycin D (AD), and of topoisomerase I with camptothecin (CPT) resulted in an increase in chromatin-bound XPG, with concomitant relocation by forming nuclear clusters. The cotranscriptional activators p300 and CREB-binding protein (CREBBP), endowed with lysine acetyl transferase (KAT) activity, interact with and acetylate XPG. Depletion of both KATs by RNA interference, or chemical inhibition with C646, significantly reduced XPG acetylation. However, the loss of KAT activity also resulted in increased chromatin association and the relocation of XPG, indicating that these processes were induced by transcriptional stress and not by reduced acetylation. Transcription inhibitors, including C646, triggered the R-loop formation and phosphorylation of histone H2AX (γ-H2AX). Proximity ligation assay (PLA) showed that XPG colocalized with R-loops, indicating the recruitment of the protein to these structures. These results suggest that transcriptional stress-induced XPG relocation may represent recruitment to sites of R-loop processing.
Collapse
|
15
|
Klaric JA, Wüst S, Panier S. New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response. Front Mol Biosci 2021; 8:668821. [PMID: 34026839 PMCID: PMC8138124 DOI: 10.3389/fmolb.2021.668821] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.
Collapse
Affiliation(s)
- Julie A Klaric
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stas Wüst
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stephanie Panier
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
| |
Collapse
|
16
|
Erkelenz S, Stanković D, Mundorf J, Bresser T, Claudius AK, Boehm V, Gehring NH, Uhlirova M. Ecd promotes U5 snRNP maturation and Prp8 stability. Nucleic Acids Res 2021; 49:1688-1707. [PMID: 33444449 PMCID: PMC7897482 DOI: 10.1093/nar/gkaa1274] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Pre-mRNA splicing catalyzed by the spliceosome represents a critical step in the regulation of gene expression contributing to transcriptome and proteome diversity. The spliceosome consists of five small nuclear ribonucleoprotein particles (snRNPs), the biogenesis of which remains only partially understood. Here we define the evolutionarily conserved protein Ecdysoneless (Ecd) as a critical regulator of U5 snRNP assembly and Prp8 stability. Combining Drosophila genetics with proteomic approaches, we demonstrate the Ecd requirement for the maintenance of adult healthspan and lifespan and identify the Sm ring protein SmD3 as a novel interaction partner of Ecd. We show that the predominant task of Ecd is to deliver Prp8 to the emerging U5 snRNPs in the cytoplasm. Ecd deficiency, on the other hand, leads to reduced Prp8 protein levels and compromised U5 snRNP biogenesis, causing loss of splicing fidelity and transcriptome integrity. Based on our findings, we propose that Ecd chaperones Prp8 to the forming U5 snRNP allowing completion of the cytoplasmic part of the U5 snRNP biogenesis pathway necessary to meet the cellular demand for functional spliceosomes.
Collapse
Affiliation(s)
- Steffen Erkelenz
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
| | - Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
| | - Juliane Mundorf
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Tina Bresser
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Ann-Katrin Claudius
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Volker Boehm
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany.,Institute for Genetics, University of Cologne, Cologne 50674, Germany
| | - Niels H Gehring
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany.,Institute for Genetics, University of Cologne, Cologne 50674, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
| |
Collapse
|
17
|
Wang C, Xia C, Zhu Y, Zhang H. Innovative fluorescent probes for in vivo visualization of biomolecules in living Caenorhabditis elegans. Cytometry A 2021; 99:560-574. [PMID: 33638604 DOI: 10.1002/cyto.a.24325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Caenorhabditis elegans (C. elegans) as a well-established multicellular model organism has been widely used in the biological field for half a century. Its numerous advantages including small body size, rapid life cycle, high-reproductive rate, well-defined anatomy, and conserved genome, has made C. elegans one of the most successful multicellular model organisms. Discoveries obtained from the C. elegans model have made great contributions to research fields such as development, aging, biophysics, immunology, and neuroscience. Because of its transparent body and giant cell size, C. elegans is also an ideal subject for high resolution and high-throughput optical imaging and analysis. During the past decade, great advances have been made to develop biomolecule-targeting techniques for noninvasive optical imaging. These novel technologies expanded the toolbox for qualitative and quantitative analysis of biomolecules in C. elegans. In this review, we summarize recently developed fluorescent probes or labeling techniques for visualizing biomolecules at the cellular, subcellular or molecular scale by using C. elegans as the major model organism or designed specifically for the applications in C. elegans. Combining the technological advantages of the C. elegans model with the novel fluorescent labeling techniques will provide new horizons for high-efficiency quantitative optical analysis in live organisms.
Collapse
Affiliation(s)
- Chunxia Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chujie Xia
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| |
Collapse
|
18
|
Dutertre M, Sfaxi R, Vagner S. Reciprocal Links between Pre-messenger RNA 3'-End Processing and Genome Stability. Trends Biochem Sci 2021; 46:579-594. [PMID: 33653631 DOI: 10.1016/j.tibs.2021.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
The 3'-end processing of most pre-messenger RNAs (pre-mRNAs) involves RNA cleavage and polyadenylation and is coupled to transcription termination. In both yeast and human cells, pre-mRNA 3'-end cleavage is globally inhibited by DNA damage. Recently, further links between pre-mRNA 3'-end processing and the control of genome stability have been uncovered, as reviewed here. Upon DNA damage, various genes related to the DNA damage response (DDR) escape 3'-end processing inhibition or are regulated through alternative polyadenylation (APA). Conversely, various pre-mRNA 3'-end processing factors prevent genome instability and are found at sites of DNA damage. Finally, the reciprocal link between pre-mRNA 3'-end processing and genome stability control seems important because it is conserved in evolution and involved in disease development.
Collapse
Affiliation(s)
- Martin Dutertre
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipe Labellisée Ligue Nationale Contre le Cancer.
| | - Rym Sfaxi
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipe Labellisée Ligue Nationale Contre le Cancer.
| |
Collapse
|
19
|
Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
Collapse
Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| |
Collapse
|
20
|
Yang Z, Li M, Sun Q. RHON1 Co-transcriptionally Resolves R-Loops for Arabidopsis Chloroplast Genome Maintenance. Cell Rep 2021; 30:243-256.e5. [PMID: 31914390 DOI: 10.1016/j.celrep.2019.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/24/2019] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
Preventing transcription-replication head-on conflict (HO-TRC)-triggered R-loop formation is essential for maintaining genome integrity in bacteria, plants, and mammals. The R-loop eraser RNase H can efficiently relax HO-TRCs. However, it is not clear how organisms resist HO-TRC-triggered R-loops when RNase H proteins are deficient. By screening factors that may relieve R-loop accumulation in the Arabidopsis atrnh1c mutant, we find that overexpression of the R-loop helicase RHON1 can rescue the defects of aberrantly accumulated HO-TRC-triggered R-loops co-transcriptionally. In addition, we find that RHON1 interacts with and orchestrates the transcriptional activity of plastid-encoded RNA polymerases to release the conflicts between transcription and replication. Our study illustrates that organisms employ multiple mechanisms to escape HO-TRC-triggered R-loop accumulation and thus maintain genome integrity.
Collapse
Affiliation(s)
- Zhuo Yang
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengmeng Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
21
|
Abstract
While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.
Collapse
Affiliation(s)
- Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Department of Medicine, University of Adelaide, Adelaide, SA, Australia.
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
22
|
MRE11 Is Crucial for Malaria Parasite Transmission and Its Absence Affects Expression of Interconnected Networks of Key Genes Essential for Life. Cells 2020; 9:cells9122590. [PMID: 33287434 PMCID: PMC7761864 DOI: 10.3390/cells9122590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
The meiotic recombination 11 protein (MRE11) plays a key role in DNA damage response and maintenance of genome stability. However, little is known about its function during development of the malaria parasite Plasmodium. Here, we present a functional, ultrastructural and transcriptomic analysis of Plasmodium parasites lacking MRE11 during its life cycle in both mammalian and mosquito vector hosts. Genetic disruption of Plasmodium berghei mre11 (PbMRE11) results in significant retardation of oocyst development in the mosquito midgut associated with cytoplasmic and nuclear degeneration, along with concomitant ablation of sporogony and subsequent parasite transmission. Further, absence of PbMRE11 results in significant transcriptional downregulation of genes involved in key interconnected biological processes that are fundamental to all eukaryotic life including ribonucleoprotein biogenesis, spliceosome function and iron-sulfur cluster assembly. Overall, our study provides a comprehensive functional analysis of MRE11's role in Plasmodium development during the mosquito stages and offers a potential target for therapeutic intervention during malaria parasite transmission.
Collapse
|
23
|
Ketley RF, Gullerova M. Jack of all trades? The versatility of RNA in DNA double-strand break repair. Essays Biochem 2020; 64:721-735. [PMID: 32618336 PMCID: PMC7592198 DOI: 10.1042/ebc20200008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
The mechanisms by which RNA acts in the DNA damage response (DDR), specifically in the repair of DNA double-strand breaks (DSBs), are emerging as multifaceted and complex. Different RNA species, including but not limited to; microRNA (miRNA), long non-coding RNA (lncRNA), RNA:DNA hybrid structures, the recently identified damage-induced lncRNA (dilncRNA), damage-responsive transcripts (DARTs), and DNA damage-dependent small RNAs (DDRNAs), have been shown to play integral roles in the DSB response. The diverse properties of these RNAs, such as sequence, structure, and binding partners, enable them to fulfil a variety of functions in different cellular contexts. Additionally, RNA can be modified post-transcriptionally, a process which is regulated in response to cellular stressors such as DNA damage. Many of these mechanisms are not yet understood and the literature contradictory, reflecting the complexity and expansive nature of the roles of RNA in the DDR. However, it is clear that RNA is pivotal in ensuring the maintenance of genome integrity. In this review, we will discuss and summarise recent evidence which highlights the roles of these various RNAs in preserving genomic integrity, with a particular focus on the emerging role of RNA in the DSB repair response.
Collapse
Affiliation(s)
- Ruth F Ketley
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
| |
Collapse
|
24
|
Drew K, Lee C, Cox RM, Dang V, Devitt CC, McWhite CD, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB. A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery. Dev Biol 2020; 467:108-117. [PMID: 32898505 DOI: 10.1016/j.ydbio.2020.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/18/2020] [Indexed: 01/06/2023]
Abstract
Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.
Collapse
Affiliation(s)
- Kevin Drew
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Chanjae Lee
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Rachael M Cox
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Vy Dang
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Caitlin C Devitt
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Claire D McWhite
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Ophelia Papoulas
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Ryan L Huizar
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Edward M Marcotte
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
| | - John B Wallingford
- Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
| |
Collapse
|
25
|
Tuominen I, Fuqua BK, Pan C, Renaud N, Wroblewski K, Civelek M, Clerkin K, Asaryan A, Haroutunian SG, Loureiro J, Borawski J, Roma G, Knehr J, Carbone W, French S, Parks BW, Hui ST, Mehrabian M, Magyar C, Cantor RM, Ukomadu C, Lusis AJ, Beaven SW. The Genetic Architecture of Carbon Tetrachloride-Induced Liver Fibrosis in Mice. Cell Mol Gastroenterol Hepatol 2020; 11:199-220. [PMID: 32866618 PMCID: PMC7674618 DOI: 10.1016/j.jcmgh.2020.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Liver fibrosis is a multifactorial trait that develops in response to chronic liver injury. Our aim was to characterize the genetic architecture of carbon tetrachloride (CCl4)-induced liver fibrosis using the Hybrid Mouse Diversity Panel, a panel of more than 100 genetically distinct mouse strains optimized for genome-wide association studies and systems genetics. METHODS Chronic liver injury was induced by CCl4 injections twice weekly for 6 weeks. Four hundred thirty-seven mice received CCl4 and 256 received vehicle, after which animals were euthanized for liver histology and gene expression. Using automated digital image analysis, we quantified fibrosis as the collagen proportionate area of the whole section, excluding normal collagen. RESULTS We discovered broad variation in fibrosis among the Hybrid Mouse Diversity Panel strains, demonstrating a significant genetic influence. Genome-wide association analyses revealed significant and suggestive loci underlying susceptibility to fibrosis, some of which overlapped with loci identified in mouse crosses and human population studies. Liver global gene expression was assessed by RNA sequencing across the strains, and candidate genes were identified using differential expression and expression quantitative trait locus analyses. Gene set enrichment analyses identified the underlying pathways, of which stellate cell involvement was prominent, and coexpression network modeling identified modules associated with fibrosis. CONCLUSIONS Our results provide a rich resource for the design of experiments to understand mechanisms underlying fibrosis and for rational strain selection when testing antifibrotic drugs.
Collapse
Affiliation(s)
- Iina Tuominen
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brie K Fuqua
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Calvin Pan
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Kevin Wroblewski
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Mete Civelek
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Kara Clerkin
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Ashot Asaryan
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Sara G Haroutunian
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Joseph Loureiro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jason Borawski
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | | | | | - Samuel French
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brian W Parks
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Simon T Hui
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Margarete Mehrabian
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Clara Magyar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Rita M Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Chinweike Ukomadu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Aldons J Lusis
- Departments of Medicine, Microbiology and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California.
| | - Simon W Beaven
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases at UCLA and Pfleger Liver Institute, David Geffen School of Medicine at UCLA, Los Angeles, California.
| |
Collapse
|
26
|
Lu X, Zhou Y, Meng J, Jiang L, Gao J, Cheng Y, Yan H, Wang Y, Zhang B, Li X, Yan F. RNA processing genes characterize RNA splicing and further stratify colorectal cancer. Cell Prolif 2020; 53:e12861. [PMID: 32596958 PMCID: PMC7445406 DOI: 10.1111/cpr.12861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023] Open
Abstract
Objectives Due to the limited evaluation of the prognostic value of RNA processing genes (RPGs), which are regulators of alternative splicing events (ASEs) that have been shown to be associated with tumour progression, this study sought to determine whether colorectal cancer (CRC) could be further stratified based on the expression pattern of RPGs. Materials and Methods The gene expression profiles of CRCs were collected from TCGA (training set) and three external validation cohorts, representing 1060 cases totally. Cox regression with least absolute shrinkage and selection operator (LASSO) penalty was used to develop an RNA processing gene index (RPGI) risk score. Kaplan‐Meier curves, multivariate Cox regression and restricted mean survival (RMS) analyses were harnessed to evaluate the prognostic value of the RPGI. Results A 22‐gene RPGI signature was developed, and its risk score served as a strong independent prognostic factor across all data sets when adjusted for major clinical variables. Moreover, ASEs for certain genes, such as FGFR1 and the RAS oncogene family, were significantly correlated with RPGI. Expression levels of genes involved in splicing‐ and tumour‐associated pathways were significantly correlated with RPGI score. Furthermore, a combination of RPGI with age and tumour stage resulted in significantly improved prognostic accuracy. Conclusions Our findings highlighted the prognostic value of RPGs for risk stratification of CRC patients and provide insights into specific ASEs associated with the development of CRC.
Collapse
Affiliation(s)
- Xiaofan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Yujie Zhou
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, P.R. China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, P.R. China.,Department of Pathology and Urology, University of Rochester Medical Center, Rochester, NY, USA
| | - Liyun Jiang
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Gao
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Yu Cheng
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Hangyu Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Yang Wang
- Department of Radiology, The Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, P.R. China
| | - Bing Zhang
- Department of Radiology, The Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, P.R. China
| | - Xiaobo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, P.R. China
| | - Fangrong Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| |
Collapse
|
27
|
Katahira J, Senokuchi K, Hieda M. Human THO maintains the stability of repetitive DNA. Genes Cells 2020; 25:334-342. [PMID: 32065701 DOI: 10.1111/gtc.12760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/31/2023]
Abstract
The evolutionarily conserved multiprotein complex THO/TREX is required for pre-mRNA processing, mRNA export and the maintenance of genome stability. In this study, we analyzed the genome-wide distribution of human THOC7, a component of human THO, by chromatin immunoprecipitation sequencing. The analysis revealed that human THOC7 occupies repetitive sequences, which include microsatellite repeats in genic and intergenic regions and telomeric repeats. The majority of the THOC7 ChIP peaks overlapped with those of the elongating form of RNA polymerase II and R-loops, indicating that THOC7 accumulates in transcriptionally active repeat regions. Knocking down THOC5, an RNA-binding component of human THO, by siRNA induced the accumulation of γH2AX in the repeat regions. We also observed an aberration in the telomeres in the THOC5-depleted condition. These results suggest that human THO restrains the transcription-associated instability of repeat regions in the human genome.
Collapse
Affiliation(s)
- Jun Katahira
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Kohei Senokuchi
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Miki Hieda
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Iyo-gun, Japan
| |
Collapse
|
28
|
Massonneau J, Lacombe-Burgoyne C, Boissonneault G. pH-induced variations in the TK1 gene model. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 849:503128. [PMID: 32087849 DOI: 10.1016/j.mrgentox.2019.503128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/09/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022]
Abstract
A physiological decrease in extracellular pH (pHe) alters the efficiency of DNA repair and increases formation of DNA double-strand breaks (DSBs). Whether this could translate into genetic instability and variations, was investigated using the TK6 cell model, in which positive selection of the TK1 gene loss-of-function mutations can be achieved from resistance to trifluorothymidine. Cell exposure to suboptimal pH (down to 6.9) for 3 weeks resulted in the 100 % frequency of a stronger frameshift mutation that has spread to both TK1 alleles, whereas weaker frameshift mutations within the 3'exon were eliminated during the selection. Suboptimal pHe values were also found to alter the proportion of the TK1 splicing variant expressed as percent spliced in index values and promote selection of truncated exons as well as intron retention. Although recovery at pH 7.4 did not reverse the selected frameshift mutation, reversal of splice variants and exon truncation towards control values were observed. Hence, suboptimal pHe can induce a combination of mutational events and splicing alterations within the same gene in the resistant clones. This model of positive selection for loss-of-function clearly demonstrates that suboptimal pHe may confer a similar growth advantage when such instability occurs within tumor suppressor genes.
Collapse
Affiliation(s)
- Julien Massonneau
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chloë Lacombe-Burgoyne
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Guylain Boissonneault
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
| |
Collapse
|
29
|
Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures. Sci Rep 2020; 10:28. [PMID: 31913336 PMCID: PMC6949240 DOI: 10.1038/s41598-019-56981-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
APE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368.
Collapse
|
30
|
Kawaguchi T, Rollins MG, Moinpour M, Morera AA, Ebmeier CC, Old WM, Schwartz JC. Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage. J Proteome Res 2020; 19:360-370. [PMID: 31693373 PMCID: PMC6947635 DOI: 10.1021/acs.jproteome.9b00575] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Indexed: 12/13/2022]
Abstract
The RNA-binding proteins TDP-43 and FUS are tied as the third leading known genetic cause for amyotrophic lateral sclerosis (ALS), and TDP-43 proteopathies are found in nearly all ALS patients. Both the natural function and contribution to pathology for TDP-43 remain unclear. The intersection of functions between TDP-43 and FUS can focus attention for those natural functions mostly likely to be relevant to disease. Here, we compare the role played by TDP-43 and FUS, maintaining chromatin stability for dividing HEK293T cells. We also determine and compare the interactomes of TDP-43 and FUS, quantitating changes in those before and after DNA damage. Finally, selected interactions with known importance to DNA damage repair were validated by co-immunoprecipitation assays. This study uncovered TDP-43 and FUS binding to several factors important to DNA repair mechanisms that can be replication-dependent, -independent, or both. These results provide further evidence that TDP-43 has an important role in DNA stability and provide new ways that TDP-43 can bind to the machinery that guards DNA integrity in cells.
Collapse
Affiliation(s)
- Tetsuya Kawaguchi
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Matthew G. Rollins
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Mahta Moinpour
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Andres A. Morera
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher C. Ebmeier
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - William M. Old
- Department
of Molecular and Cellular Biology, University
of Colorado, Boulder, Colorado 80309, United States
| | - Jacob C. Schwartz
- Department
of Chemistry and Biochemistry and Department of Molecular and Cellular
Biology, University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
31
|
Kostyusheva A, Brezgin S, Bayurova E, Gordeychuk I, Isaguliants M, Goptar I, Urusov F, Nikiforova A, Volchkova E, Kostyushev D, Chulanov V. ATM and ATR Expression Potentiates HBV Replication and Contributes to Reactivation of HBV Infection upon DNA Damage. Viruses 2019; 11:E997. [PMID: 31683589 PMCID: PMC6893526 DOI: 10.3390/v11110997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus infection (CHB) caused by the hepatitis B virus (HBV) is one of the most common viral infections in the world. Reactivation of HBV infection is a life-threatening condition observed in patients with CHB receiving chemotherapy or other medications. Although HBV reactivation is commonly attributed to immune suppression, other factors have long been suspected to play a role, including intracellular signaling activated in response to DNA damage. We investigated the effects of DNA-damaging factors (doxorubicin and hydrogen peroxide) on HBV reactivation/replication and the consequent DNA-damage response. Dose-dependent activation of HBV replication was observed in response to doxorubicin and hydrogen peroxide which was associated with a marked elevation in the mRNA levels of ataxia-telangiectasia mutated (ATM) and ATM- and RAD3-related (ATR) kinases. Downregulation of ATM or ATR expression by shRNAs substantially reduced the levels of HBV RNAs and DNA. In contrast, transcriptional activation of ATM or ATR using CRISPRa significantly increased HBV replication. We conclude that ATM and ATR are essential for HBV replication. Furthermore, DNA damage leading to the activation of ATM and ATR transcription, results in the reactivation of HBV replication.
Collapse
Affiliation(s)
- Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
- Institute of Immunology, Federal Medical Biological Agency, Moscow 115522, Russia.
| | - Ekaterina Bayurova
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Ilya Gordeychuk
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
| | - Maria Isaguliants
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
| | - Irina Goptar
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Felix Urusov
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Anastasiya Nikiforova
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Elena Volchkova
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
- Central Research Institute of Epidemiology, Moscow 111123, Russia.
| |
Collapse
|
32
|
Jiménez M, Urtasun R, Elizalde M, Azkona M, Latasa MU, Uriarte I, Arechederra M, Alignani D, Bárcena-Varela M, Álvarez-Sola G, Colyn L, Santamaría E, Sangro B, Rodriguez-Ortigosa C, Fernández-Barrena MG, Ávila MA, Berasain C. Splicing events in the control of genome integrity: role of SLU7 and truncated SRSF3 proteins. Nucleic Acids Res 2019; 47:3450-3466. [PMID: 30657957 PMCID: PMC6468163 DOI: 10.1093/nar/gkz014] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/21/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
Genome instability is related to disease development and carcinogenesis. DNA lesions are caused by genotoxic compounds but also by the dysregulation of fundamental processes like transcription, DNA replication and mitosis. Recent evidence indicates that impaired expression of RNA-binding proteins results in mitotic aberrations and the formation of transcription-associated RNA-DNA hybrids (R-loops), events strongly associated with DNA injury. We identify the splicing regulator SLU7 as a key mediator of genome stability. SLU7 knockdown results in R-loops formation, DNA damage, cell-cycle arrest and severe mitotic derangements with loss of sister chromatid cohesion (SCC). We define a molecular pathway through which SLU7 keeps in check the generation of truncated forms of the splicing factor SRSF3 (SRp20) (SRSF3-TR). Behaving as dominant negative, or by gain-of-function, SRSF3-TR impair the correct splicing and expression of the splicing regulator SRSF1 (ASF/SF2) and the crucial SCC protein sororin. This unique function of SLU7 was found in cancer cells of different tissue origin and also in the normal mouse liver, demonstrating a conserved and fundamental role of SLU7 in the preservation of genome integrity. Therefore, the dowregulation of SLU7 and the alterations of this pathway that we observe in the cirrhotic liver could be involved in the process of hepatocarcinogenesis.
Collapse
Affiliation(s)
- Maddalen Jiménez
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Raquel Urtasun
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain
| | - María Elizalde
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - María Azkona
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - M Ujue Latasa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - María Arechederra
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Diego Alignani
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,Cytometry Unit, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Gloria Álvarez-Sola
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Leticia Colyn
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Eva Santamaría
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Bruno Sangro
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain.,Hepatology Unit, Navarra University Clinic, Pamplona 31008, Spain
| | - Carlos Rodriguez-Ortigosa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maite G Fernández-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| |
Collapse
|
33
|
Siebenwirth C, Greubel C, Drexler GA, Reindl J, Walsh DWM, Schwarz B, Sammer M, Baur I, Pospiech H, Schmid TE, Dollinger G, Friedl AA. Local inhibition of rRNA transcription without nucleolar segregation after targeted ion irradiation of the nucleolus. J Cell Sci 2019; 132:jcs.232181. [PMID: 31492757 PMCID: PMC6803363 DOI: 10.1242/jcs.232181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
Nucleoli have attracted interest for their role as cellular stress sensors and as potential targets for cancer treatment. The effect of DNA double-strand breaks (DSBs) in nucleoli on rRNA transcription and nucleolar organisation appears to depend on the agent used to introduce DSBs, DSB frequency and the presence (or not) of DSBs outside the nucleoli. To address the controversy, we targeted nucleoli with carbon ions at the ion microbeam SNAKE. Localized ion irradiation with 1-100 carbon ions per point (about 0.3-30 Gy per nucleus) did not lead to overall reduced ribonucleotide incorporation in the targeted nucleolus or other nucleoli of the same cell. However, both 5-ethynyluridine incorporation and Parp1 protein levels were locally decreased at the damaged nucleolar chromatin regions marked by γH2AX, suggesting localized inhibition of rRNA transcription. This locally restricted transcriptional inhibition was not accompanied by nucleolar segregation, a structural reorganisation observed after inhibition of rRNA transcription by treatment with actinomycin D or UV irradiation. The presented data indicate that even multiple complex DSBs do not lead to a pan-nucleolar response if they affect only a subnucleolar region.
Collapse
Affiliation(s)
- Christian Siebenwirth
- Bundeswehr Institute of Radiobiology, 80937 Munich, Germany .,Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany.,Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Christoph Greubel
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Guido A Drexler
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Judith Reindl
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Dietrich W M Walsh
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Benjamin Schwarz
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Matthias Sammer
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Iris Baur
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Thomas E Schmid
- Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Günther Dollinger
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| |
Collapse
|
34
|
Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
Collapse
Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
35
|
Pillon MC, Lo YH, Stanley RE. IT'S 2 for the price of 1: Multifaceted ITS2 processing machines in RNA and DNA maintenance. DNA Repair (Amst) 2019; 81:102653. [PMID: 31324529 PMCID: PMC6764878 DOI: 10.1016/j.dnarep.2019.102653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cells utilize sophisticated RNA processing machines to ensure the quality of RNA. Many RNA processing machines have been further implicated in regulating the DNA damage response signifying a strong link between RNA processing and genome maintenance. One of the most intricate and highly regulated RNA processing pathways is the processing of the precursor ribosomal RNA (pre-rRNA), which is paramount for the production of ribosomes. Removal of the Internal Transcribed Spacer 2 (ITS2), located between the 5.8S and 25S rRNA, is one of the most complex steps of ribosome assembly. Processing of the ITS2 is initiated by the newly discovered endoribonuclease Las1, which cleaves at the C2 site within the ITS2, generating products that are further processed by the polynucleotide kinase Grc3, the 5'→3' exonuclease Rat1, and the 3'→5' RNA exosome complex. In addition to their defined roles in ITS2 processing, these critical cellular machines participate in other stages of ribosome assembly, turnover of numerous cellular RNAs, and genome maintenance. Here we summarize recent work defining the molecular mechanisms of ITS2 processing by these essential RNA processing machines and highlight their emerging roles in transcription termination, heterochromatin function, telomere maintenance, and DNA repair.
Collapse
Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Yu-Hua Lo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
36
|
Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
Collapse
Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| |
Collapse
|
37
|
Burger K, Ketley RF, Gullerova M. Beyond the Trinity of ATM, ATR, and DNA-PK: Multiple Kinases Shape the DNA Damage Response in Concert With RNA Metabolism. Front Mol Biosci 2019; 6:61. [PMID: 31428617 PMCID: PMC6688092 DOI: 10.3389/fmolb.2019.00061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/22/2022] Open
Abstract
Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.
Collapse
Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
38
|
Awasthi S, Verma M, Mahesh A, K Khan MI, Govindaraju G, Rajavelu A, Chavali PL, Chavali S, Dhayalan A. DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. Nucleic Acids Res 2019; 46:6304-6317. [PMID: 29618122 PMCID: PMC6158705 DOI: 10.1093/nar/gky231] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 12/19/2022] Open
Abstract
Among the proteins predicted to be a part of the DExD box RNA helicase family, the functions of DDX49 are unknown. Here, we characterize the enzymatic activities and functions of DDX49 by comparing its properties with the well-studied RNA helicase, DDX39B. We find that DDX49 exhibits a robust ATPase and RNA helicase activity, significantly higher than that of DDX39B. DDX49 is required for the efficient export of poly (A)+ RNA from nucleus in a splicing-independent manner. Furthermore, DDX49 is a resident protein of nucleolus and regulates the steady state levels of pre-ribosomal RNA by regulating its transcription and stability. These dual functions of regulating mRNA export and pre-ribosomal RNA levels enable DDX49 to modulate global translation. Phenotypically, DDX49 promotes proliferation and colony forming potential of cells. Strikingly, DDX49 is significantly elevated in diverse cancer types suggesting that the increased abundance of DDX49 has a role in oncogenic transformation of cells. Taken together, this study shows the physiological role of DDX49 in regulating distinct steps of mRNA and pre-ribosomal RNA metabolism and hence translation and potential pathological role of its dysregulation, especially in cancers.
Collapse
Affiliation(s)
- Sharad Awasthi
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Mamta Verma
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arun Mahesh
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Bacterial and Parasite Disease Biology, Rajiv Gandhi Center for Biotechnology, Trivandrum 695 014, India
| | - Arumugam Rajavelu
- Bacterial and Parasite Disease Biology, Rajiv Gandhi Center for Biotechnology, Trivandrum 695 014, India
| | - Pavithra L Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| |
Collapse
|
39
|
Shen L, Wang Q, Liu R, Chen Z, Zhang X, Zhou P, Wang Z. LncRNA lnc-RI regulates homologous recombination repair of DNA double-strand breaks by stabilizing RAD51 mRNA as a competitive endogenous RNA. Nucleic Acids Res 2019; 46:717-729. [PMID: 29216366 PMCID: PMC5778505 DOI: 10.1093/nar/gkx1224] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/25/2017] [Indexed: 12/11/2022] Open
Abstract
DNA double-strand break (DSB) repair is critical for the maintenance of genome stability. The current models of the mechanism of DSB repair are based on studies of DNA repair proteins. Long non-coding RNAs (lncRNAs) have recently emerged as new regulatory molecules, with diverse functions in biological processes. In the present study, we found that expression of the ionizing radiation-inducible lncRNA, lnc-RI, was correlate negatively with micronucleus frequencies in human peripheral blood lymphocytes. Knockdown of lnc-RI significantly increased spontaneous DSBs levels, which was confirmed to be associated with the decreased efficiency of homologous recombination (HR) repair of DSBs. The expression of RAD51, a key recombinase in the HR pathway, decreased sharply in lnc-RI-depressed cells. In a further investigation, we demonstrated that miR-193a-3p could bind with both lnc-RI and RAD51 mRNA and depressed the expression of lnc-RI and RAD51 mRNA. Lnc-RI acted as a competitive endogenous RNA (ceRNA) to stabilize RAD51 mRNA via competitive binding with miR-193a-3p and release of its inhibition of RAD51 expression. To our knowledge, this is the first study to demonstrate the role of lnc-RI in regulating HR repair of DSBs. The feedback loop established in the current study suggests that lnc-RI is critical for the maintenance of genomic stability.
Collapse
Affiliation(s)
- Liping Shen
- School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, Jiangsu 215123, PR China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Qi Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Ruixue Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Zhongmin Chen
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Xueqing Zhang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Pingkun Zhou
- School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, Jiangsu 215123, PR China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Zhidong Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| |
Collapse
|
40
|
Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
Collapse
Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
| |
Collapse
|
41
|
Chi B, O'Connell JD, Iocolano AD, Coady JA, Yu Y, Gangopadhyay J, Gygi SP, Reed R. The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex. Nucleic Acids Res 2019; 46:11939-11951. [PMID: 30398641 PMCID: PMC6294556 DOI: 10.1093/nar/gky1093] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular pathways disrupted in motor neuron diseases is urgently needed. Here, we employed CRISPR knockout (KO) to investigate the functions of four ALS-causative RNA/DNA binding proteins (FUS, EWSR1, TAF15 and MATR3) within the RNAP II/U1 snRNP machinery. We found that each of these structurally related proteins has distinct roles with FUS KO resulting in loss of U1 snRNP and the SMN complex, EWSR1 KO causing dissociation of the tRNA ligase complex, and TAF15 KO resulting in loss of transcription factors P-TEFb and TFIIF. However, all four ALS-causative proteins are required for association of the ASC-1 transcriptional co-activator complex with the RNAP II/U1 snRNP machinery. Remarkably, mutations in the ASC-1 complex are known to cause a severe form of Spinal Muscular Atrophy (SMA), and we show that an SMA-causative mutation in an ASC-1 component or an ALS-causative mutation in FUS disrupts association between the ASC-1 complex and the RNAP II/U1 snRNP machinery. We conclude that ALS and SMA are more intimately tied to one another than previously thought, being linked via the ASC-1 complex.
Collapse
Affiliation(s)
- Binkai Chi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Jeremy D O'Connell
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Alexander D Iocolano
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Jordan A Coady
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Jaya Gangopadhyay
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA
| |
Collapse
|
42
|
Han G, Zhao J, Zhang R, Tian X, Liu Z, Wang A, Liu R, Liu B, Han M, Gao X, Zhang Z. Membrane‐Penetrating Carbon Quantum Dots for Imaging Nucleic Acid Structures in Live Organisms. Angew Chem Int Ed Engl 2019; 58:7087-7091. [DOI: 10.1002/anie.201903005] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Guangmei Han
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 China
| | - Jun Zhao
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Xiaohe Tian
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Zhengjie Liu
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Aidong Wang
- School of Chemistry and Chemical EngineeringHuangshan University Huangshan Anhui 245041 China
| | - Renyong Liu
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Bianhua Liu
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Ming‐Yong Han
- Institute of Materials Research and EngineeringA-STAR 3 Research Link 117602 Singapore
| | - Xiaohu Gao
- Department of BioengineeringUniversity of Washington Seattle WA 98195 USA
| | - Zhongping Zhang
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 China
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| |
Collapse
|
43
|
Zeng W, Du Z, Luo Q, Zhao Y, Wang Y, Wu K, Jia F, Zhang Y, Wang F. Proteomic Strategy for Identification of Proteins Responding to Cisplatin-Damaged DNA. Anal Chem 2019; 91:6035-6042. [PMID: 30990031 DOI: 10.1021/acs.analchem.9b00554] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new proteomic strategy combining functionalized magnetic nanoparticle affinity probes with mass spectrometry was developed to capture and identify proteins specifically responding to 1,2-d(GpG) intrastrand cisplatin-cross-linked DNA, the major DNA lesion caused by cisplatin and thought to induce apoptosis. A 16-mer oligodeoxynucleotide (ODN) duplex and its cisplatin-cross-linked adduct were immobilized on magnetic nanoparticles via click reaction, respectively, to fabricate negative and positive affinity probes which were very stable in cellular protein extracts due to the excellent bio-orthogonality of click chemistry and the inertness of covalent triazole linker. Quantitative mass spectrometry results unambiguously revealed the predominant binding of HMGB1 and HMGB2, the well-established specific binders of 1,2-cisplatin-cross-linked DNA, to the cisplatin-cross-linked ODN, thus validating the accuracy and reliability of our strategy. Furthermore, 5 RNA or single-stranded DNA binding proteins, namely, hnRNP A/B, RRP44, RL30, RL13, and NCL, were demonstrated to recognize specifically the cisplatinated ODN, indicating the significantly unwound ODN duplex by cisplatin cross-linking. In contrast, the binding of a transcription factor TFIIFa to DNA was retarded due to cisplatin damage, implying that the cisplatin lesion stalls DNA transcription. These findings promote understanding in the cellular responses to cisplatin-damaged DNA and inspire further precise elucidation of the action mechanism of cisplatin.
Collapse
Affiliation(s)
- Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhifeng Du
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Yuanyuan Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Basic Medical College , Shandong University of Chinese Traditional Medicine , Jinan 250355 , P. R. China
| |
Collapse
|
44
|
Han G, Zhao J, Zhang R, Tian X, Liu Z, Wang A, Liu R, Liu B, Han M, Gao X, Zhang Z. Membrane‐Penetrating Carbon Quantum Dots for Imaging Nucleic Acid Structures in Live Organisms. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guangmei Han
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 China
| | - Jun Zhao
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Xiaohe Tian
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Zhengjie Liu
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| | - Aidong Wang
- School of Chemistry and Chemical EngineeringHuangshan University Huangshan Anhui 245041 China
| | - Renyong Liu
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Bianhua Liu
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
| | - Ming‐Yong Han
- Institute of Materials Research and EngineeringA-STAR 3 Research Link 117602 Singapore
| | - Xiaohu Gao
- Department of BioengineeringUniversity of Washington Seattle WA 98195 USA
| | - Zhongping Zhang
- Institute of Intelligent MachinesChinese Academy of Sciences Hefei Anhui 230031 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 China
- School of Chemistry and Chemical Engineering, and Institute of Physical Science and Information TechnologyAnhui University Hefei Anhui 230601 China
| |
Collapse
|
45
|
Chuang TW, Lu CC, Su CH, Wu PY, Easwvaran S, Lee CC, Kuo HC, Hung KY, Lee KM, Tsai CY, Tarn WY. The RNA Processing Factor Y14 Participates in DNA Damage Response and Repair. iScience 2019; 13:402-415. [PMID: 30901577 PMCID: PMC6428943 DOI: 10.1016/j.isci.2019.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 02/01/2023] Open
Abstract
DNA repair deficiency leads to genome instability and hence human disease. Depletion of the RNA processing factor Y14/RBM8A in cultured cells or Rbm8a haplodeficiency in the developing mouse cortex results in the accumulation of DNA damage. Y14 depletion differentially affected the expression of DNA damage response (DDR) factors and induced R-loops, both of which threaten genomic stability. Immunoprecipitation coupled with mass spectrometry revealed DDR factors as potential Y14-interacting partners. Further results confirmed that Y14 interacts with Ku and several DDR factors in an ATM-dependent manner. Y14 co-fractionated with Ku in chromatin-enriched fractions and further accumulated on chromatin upon DNA damage. Y14 knockdown delayed recruitment of DDR factors to DNA damage sites and formation of γH2AX foci and also led to Ku retention on chromatin. Accordingly, Y14 depletion compromised the efficiency of DNA end joining. Therefore Y14 likely plays a direct role in DNA damage repair via its interaction with DDR factors. Y14 deficiency leads to DNA damage accumulation Y14 depletion disturbs DNA damage response and induces R-loops Y14 promotes Ku70/80 recruitment to DNA damage sites Y14 participates in DNA damage repair
Collapse
Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Chun-Hao Su
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Pei-Yu Wu
- Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
| | - Sarasvathi Easwvaran
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chi-Chieh Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Hung-Che Kuo
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuan-Yang Hung
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Ching-Yen Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan.
| |
Collapse
|
46
|
White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. Proc Natl Acad Sci U S A 2019; 116:4446-4455. [PMID: 30782839 DOI: 10.1073/pnas.1819778116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans.
Collapse
|
47
|
Li S, Li R, Ma Y, Zhang C, Huang T, Zhu S. Transcriptome analysis of differentially expressed genes and pathways associated with mitoxantrone treatment prostate cancer. J Cell Mol Med 2018; 23:1987-2000. [PMID: 30592148 PMCID: PMC6378179 DOI: 10.1111/jcmm.14100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
The global physiological function of specifically expressed genes of mitoxantrone (MTX)‐resistant prostate cancer (PCa) is unclear. In this study, gene expression pattern from microarray data was investigated for identifying differentially expressed genes (DEGs) in MTX‐resistant PCa xenografts. Human PCa cell lines DU145 and PC3 were cultured in vitro and xenografted into severe combined immunodeficiency (SCID) mice, treated with MTX intragastrically, three times a week until all mice relapsed. Gene expression profiles of the xenografts from castrated mice were performed with Affymetrix human whole genomic oligonucleotide microarray. The Cytoscape software was used to investigate the relationship between proteins and the signalling transduction network. A total of 355 overlapping genes were differentially expressed in MTX‐resistant DU145R and PC3R xenografts. Of these, 16 genes were selected to be validated by quantitative real‐time PCR (qRT‐PCR) in these xenografts, and further tested in a set of formalin‐fixed, paraffin‐embedded and optimal cutting temperature (OCT) clinical tumour samples. Functional and pathway enrichment analyses revealed that these DEGs were closely related to cellular activity, androgen synthesis, DNA damage and repair, also involved in the ERK/MAPK, PI3K/serine‐threonine protein kinase, also known as protein kinase B, PKB (AKT) and apoptosis signalling pathways. This exploratory analysis provides information about potential candidate genes and may bring new insights into the molecular cascade involvement in MTX‐resistant PCa.
Collapse
Affiliation(s)
- Sanqiang Li
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Medical College, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ruifang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan, China
| | - Yu Ma
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Cong Zhang
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tao Huang
- Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Sha Zhu
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Collaborative Innovation Center of Cancer Chemoprevention, Zhengzhou, Henan, China
| |
Collapse
|
48
|
Makharashvili N, Arora S, Yin Y, Fu Q, Wen X, Lee JH, Kao CH, Leung JWC, Miller KM, Paull TT. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. eLife 2018; 7:e42733. [PMID: 30523780 PMCID: PMC6296784 DOI: 10.7554/elife.42733] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023] Open
Abstract
The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5' flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.
Collapse
Affiliation(s)
- Nodar Makharashvili
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Sucheta Arora
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Yizhi Yin
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Qiong Fu
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Xuemei Wen
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Ji-Hoon Lee
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Chung-Hsuan Kao
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Justin WC Leung
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockUnited States
| | - Kyle M Miller
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Tanya T Paull
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| |
Collapse
|
49
|
Black EM, Giunta S. Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases. Genes (Basel) 2018; 9:E615. [PMID: 30544645 PMCID: PMC6315641 DOI: 10.3390/genes9120615] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Maintenance of an intact genome is essential for cellular and organismal homeostasis. The centromere is a specialized chromosomal locus required for faithful genome inheritance at each round of cell division. Human centromeres are composed of large tandem arrays of repetitive alpha-satellite DNA, which are often sites of aberrant rearrangements that may lead to chromosome fusions and genetic abnormalities. While the centromere has an essential role in chromosome segregation during mitosis, the long and repetitive nature of the highly identical repeats has greatly hindered in-depth genetic studies, and complete annotation of all human centromeres is still lacking. Here, we review our current understanding of human centromere genetics and epigenetics as well as recent investigations into the role of centromere DNA in disease, with a special focus on cancer, aging, and human immunodeficiency⁻centromeric instability⁻facial anomalies (ICF) syndrome. We also highlight the causes and consequences of genomic instability at these large repetitive arrays and describe the possible sources of centromere fragility. The novel connection between alpha-satellite DNA instability and human pathological conditions emphasizes the importance of obtaining a truly complete human genome assembly and accelerating our understanding of centromere repeats' role in physiology and beyond.
Collapse
Affiliation(s)
- Elizabeth M Black
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
50
|
Devecchi A, De Cecco L, Dugo M, Penso D, Dagrada G, Brich S, Stacchiotti S, Sensi M, Canevari S, Pilotti S. The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial-mesenchymal transition, and immune response. Cancer Commun (Lond) 2018; 38:70. [PMID: 30486883 PMCID: PMC6260689 DOI: 10.1186/s40880-018-0339-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, and poorly investigated simple sarcoma with a low frequency of genetic deregulation other than an Ewing sarcoma RNA binding protein 1 (EWSR1)-Wilm's tumor suppressor (WT1) translocation. We used whole-exome sequencing to interrogate six consecutive pre-treated DSRCTs whose gene expression was previously investigated. METHODS DNA libraries were prepared from formalin-fixed, paraffin-embedded archival tissue specimens following the Agilent SureSelectXT2 target enrichment protocol and sequenced on Illumina NextSeq 500. Raw sequence data were aligned to the reference genome with Burrows-Wheeler Aligner algorithm. Somatic mutations and copy number alterations (CNAs) were identified using MuTect2 and EXCAVATOR2, respectively. Biological functions associated with altered genes were investigated through Ingenuity Pathway Analysis (IPA) software. RESULTS A total of 137 unique somatic mutations were identified: 133 mutated genes were case-specific, and 2 were mutated in two cases but in different positions. Among the 135 mutated genes, 27% were related to two biological categories: DNA damage-response (DDR) network that was also identified through IPA and mesenchymal-epithelial reverse transition (MErT)/epithelial-mesenchymal transition (EMT) already demonstrated to be relevant in DSRCT. The mutated genes in the DDR network were involved in various steps of transcription and particularly affected pre-mRNA. Half of these genes encoded RNA-binding proteins or DNA/RNA-binding proteins, which were recently recognized as a new class of DDR players. CNAs in genes/gene families, involved in MErT/EMT and DDR, were recurrent across patients and mostly segregated in the MErT/EMT category. In addition, recurrent gains of regions in chromosome 1 involving many MErT/EMT gene families and loss of one arm or the entire chromosome 6 affecting relevant immune-regulatory genes were recorded. CONCLUSIONS The emerging picture is an extreme inter-tumor heterogeneity, characterized by the concurrent deregulation of the DDR and MErT/EMT dynamic and plastic programs that could favour genomic instability and explain the refractory DSRCT profile.
Collapse
Affiliation(s)
- Andrea Devecchi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Matteo Dugo
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Donata Penso
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Gianpaolo Dagrada
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Silvia Brich
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Silvia Stacchiotti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Marialuisa Sensi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy
| | - Silvana Canevari
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 2133, Milan, Italy.
| | - Silvana Pilotti
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy.
| |
Collapse
|